public class ObjectStringDNASeqDist extends ObjectStringEditDist
LocalAbstractObject.DataEqualObject, LocalAbstractObject.TextStreamFactory<T extends LocalAbstractObject>, LocalAbstractObject.TrivialDistanceFunction
text
counterDistanceComputations, counterLowerBoundDistanceComputations, counterPrecomputedDistanceSavings, counterUpperBoundDistanceComputations, MAX_DISTANCE, MIN_DISTANCE, suppData, trivialDistanceFunction, UNKNOWN_DISTANCE
Constructor and Description |
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ObjectStringDNASeqDist()
Creates a new instance of Object random generated
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ObjectStringDNASeqDist(java.io.BufferedReader stream)
Creates a new instance of Object from stream
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ObjectStringDNASeqDist(int minLength,
int maxLength)
Creates a new instance of Object random generated
with minimal length equal to minLength and maximal
length equal to maxLength
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ObjectStringDNASeqDist(java.lang.String text)
Creates a new instance of Object
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Modifier and Type | Method and Description |
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protected float |
getDistanceUpperBoundImpl(LocalAbstractObject obj,
int accuracy)
Implementation that actually computes the upper bound on the metric distance.
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protected int |
getChangeWeight(char chr1,
char chr2)
Returns the weight of changing
char1 into char2 during
the edit distance computation. |
protected int |
getInsertDeleteWeight()
Returns the weight of deleting or inserting a character during
the edit distance computation.
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getDistanceImpl, getDistanceLowerBoundImpl
binarySerialize, cloneRandomlyModify, dataEquals, dataHashCode, generateRandom, getBinarySize, getObjectKey, getSize, getStringData, getStringLength, toString, writeData
clearSurplusData, clone, clone, create, create, createMetaDistancesHolder, excludeUsingPrecompDist, getDistance, getDistance, getDistance, getDistanceFilter, getDistanceFilter, getDistanceFilter, getDistanceFilter, getDistanceLowerBound, getDistanceStorePrecomputed, getDistanceStorePrecomputed, getDistanceStorePrecomputed, getDistanceUpperBound, getFieldsForNames, getMaxDistance, getNormDistance, getPrecomputedDistance, getPrecomputedDistance, getRandomChar, getRandomNormal, chainDestroy, chainFilter, includeUsingPrecompDist, isDistanceCompatible, parseObjectComment, peekNextChar, readAttributesFromStream, readObjectComments, readObjectCommentsWithoutData, unchainFilter, write, write, writeAttributesToStream, writeObjectComment
clone, getLocatorURI, getNoDataObject, getObjectKey, getObjectLocatorURI, setObjectKey
public ObjectStringDNASeqDist(java.lang.String text)
public ObjectStringDNASeqDist()
public ObjectStringDNASeqDist(int minLength, int maxLength)
public ObjectStringDNASeqDist(java.io.BufferedReader stream) throws java.io.IOException
java.io.IOException
protected int getInsertDeleteWeight()
ObjectStringEditDist
getInsertDeleteWeight
in class ObjectStringEditDist
protected int getChangeWeight(char chr1, char chr2)
ObjectStringEditDist
char1
into char2
during
the edit distance computation. The returned value must be greater than or
equal to zero and must be symmetric, that is getChangeWeight(x,y) == getChangeWeight(y,x)
.getChangeWeight
in class ObjectStringEditDist
chr1
- the source characterchr2
- the target characterchar1
into char2
protected float getDistanceUpperBoundImpl(LocalAbstractObject obj, int accuracy)
LocalAbstractObject
getDistanceUpperBoundImpl
in class ObjectStringEditDist
obj
- the object to compute upper-bound distance toaccuracy
- the level of precision to use for upper-boundobj